photobiology (version 0.13.1)

find_peaks: Find local maxima or global maximum (peaks)

Description

These functions find peaks (local maxima) and valleys (local minima) in a numeric vector, using a user selectable span and global and local size thresholds, returning a logical vector.

Usage

find_peaks(
  x,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  span = 3,
  strict = FALSE,
  na.rm = FALSE
)
find_valleys(
  x,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  span = 3,
  strict = FALSE,
  na.rm = FALSE
)

Value

A vector of logical values of the same length as x. Values that are TRUE correspond to local peaks in vector x and can be used to extract the rows corresponding to peaks from a data frame.

Arguments

x

numeric vector. Hint: to find valleys, change the sign of the argument with the unnary operator -.

global.threshold

numeric A value belonging to class "AsIs" is interpreted as an absolute minimum height or depth expressed in data units. A bare numeric value (normally between 0.0 and 1.0), is interpreted as relative to threshold.range. In both cases it sets a global height (depth) threshold below which peaks (valleys) are ignored. A bare negative numeric value indicates the global height (depth) threshold below which peaks (valleys) are be ignored. If global.threshold = NULL, no threshold is applied and all peaks returned.

local.threshold

numeric A value belonging to class "AsIs" is interpreted as an absolute minimum height (depth) expressed in data units relative to a within-window computed reference value. A bare numeric value (normally between 0.0 and 1.0), is interpreted as expressed in units relative to threshold.range. In both cases local.threshold sets a local height (depth) threshold below which peaks (valleys) are ignored. If local.threshold = NULL or if span spans the whole of x, no threshold is applied.

local.reference

character One of "median" or "farthest". The reference used to assess the height of the peak, either the minimum/maximum value within the window or the median of all values in the window.

threshold.range

numeric vector If of length 2 or a longer vector range(threshold.range) is used to scale both thresholds. With NULL, the default, range(x) is used, and with a vector of length one range(threshold.range, x) is used, i.e., the range is expanded.

span

odd positive integer A peak is defined as an element in a sequence which is greater than all other elements within a moving window of width span centred at that element. The default value is 5, meaning that a peak is taller than its four nearest neighbours. span = NULL extends the span to the whole length of x.

strict

logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: FALSE (since version 0.13.1).

na.rm

logical indicating whether NA values should be stripped before searching for peaks.

Details

Function find_peaks is a wrapper built onto function peaks from splus2R, adds support for peak height thresholds and handles span = NULL and non-finite (including NA) values differently than splus2R::peaks. Instead of giving an error when na.rm = FALSE and x contains NA values, NA values are replaced with the smallest finite value in x. span = NULL is treated as a special case and selects max(x). Passing `strict = TRUE` ensures that multiple global and within window maxima are ignored, and can result in no peaks being returned.

Two tests make it possible to ignore irrelevant peaks. One test (global.threshold) is based on the absolute height of the peaks and can be used in all cases to ignore globally low peaks. A second test (local.threshold) is available when the window defined by `span` does not include all observations and can be used to ignore peaks that are not locally prominent. In this second approach the height of each peak is compared to a summary computed from other values within the window of width equal to span where it was found. In this second case, the reference value used within each window containing a peak is given by local.reference. Parameter threshold.range determines how the values passed as argument to global.threshold and local.threshold are scaled. The default, NULL uses the range of x. Thresholds for ignoring too small peaks are applied after peaks are searched for, and threshold values can in some cases result in no peaks being returned.

While functions find_peaks and find_valleys() accept as input a numeric vector and return a logical vector, methods peaks and valleys accept as input different R objects, including spectra and collections of spectra and return a subset of the object. These methods are implemented using calls to functions find_peaks and fit_peaks.

See Also

peaks.

Other peaks and valleys functions: find_spikes(), get_peaks(), peaks(), replace_bad_pixs(), spikes(), valleys(), wls_at_target()

Examples

with(sun.data, which(find_peaks(s.e.irrad, span = NULL)))
with(sun.data, which(find_peaks(s.e.irrad, span = 51)))
with(sun.data, w.length[find_peaks(s.e.irrad, span = 51)])
with(sun.data, sum(find_peaks(s.e.irrad, span = NULL, strict = TRUE)))

with(sun.data, which(find_valleys(s.e.irrad, span = NULL)))
with(sun.data, which(find_valleys(s.e.irrad, span = 51)))